Attempt to fix test conversion step in CI #7
Workflow file for this run
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| name: Build Package | |
| on: | |
| push: | |
| branches: '*' | |
| pull_request: | |
| branches: ['main'] | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v1 | |
| - name: Set up Python 3.6 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.6' | |
| - name: Install dependencies | |
| run: pip install wheel setuptools | |
| - name: Build package | |
| run: python setup.py bdist_wheel | |
| - name: Upload Python wheel | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: "Python wheel" | |
| path: ./dist/* | |
| if-no-files-found: error | |
| tests: | |
| needs: build | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [windows-latest, ubuntu-latest, macos-latest] | |
| python: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v1 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: pip install wheel setuptools | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: "Python wheel" | |
| - name: Install wheel | |
| run: pip install --find-links=. vsi2tif-* | |
| shell: bash | |
| - name: Test CLI | |
| run: vsi2tif --help | |
| shell: bash | |
| test-convert: | |
| needs: build | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v1 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: "Python wheel" | |
| - name: Install wheel | |
| run: pip install --find-links=. vsi2tif-* | |
| shell: bash | |
| - name: Install vips | |
| run: brew install vips | |
| - name: Download bftools | |
| run: | | |
| wget http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip | |
| unzip bftools.zip | |
| - name: Convert WSI | |
| run: | | |
| wget https://openslide.cs.cmu.edu/download/openslide-testdata/Olympus/OS-1.zip | |
| unzip OS-1.zip | |
| - name: Test conversion | |
| run: vsi2tif -i ./OS-1/ -o ./output/ -b bftools/bfconvert | |
| shell: bash |